Mary Petrone
About
Research
Publications
2025
Tunicate metatranscriptomes reveal evidence of ancient co-divergence between viruses and their hosts
Petrone M, Grove J, Parry R, Van Brussel K, Mifsud J, Dindar Z, Mei S, Shi M, Turnbull O, Marzinelli E, Holmes E. Tunicate metatranscriptomes reveal evidence of ancient co-divergence between viruses and their hosts. Current Biology 2025, 35: 3035-3047.e4. PMID: 40472852, DOI: 10.1016/j.cub.2025.05.032.Peer-Reviewed Original ResearchRNA virusesCo-divergenceEvolution of structural genesVirus-host co-divergenceRNA-dependent RNA polymeraseRNA virus evolutionNegative-sense virusesPhylogenetic relationshipsSister groupEarly chordatesRNA polymeraseStructural geneAnimal evolutionEvolutionary historyTransitional taxaRNA librariesEvolutionary timescalesInvertebrate relativesVirus evolutionVirus lineagesMultiple lineagesRNAVertebratesChordatesTunicates
2024
A virus associated with the zoonotic pathogen Plasmodium knowlesi causing human malaria is a member of a diverse and unclassified viral taxon
Petrone M, Charon J, Grigg M, William T, Rajahram G, Westaway J, Piera K, Shi M, Anstey N, Holmes E. A virus associated with the zoonotic pathogen Plasmodium knowlesi causing human malaria is a member of a diverse and unclassified viral taxon. Virus Evolution 2024, 10: veae091. PMID: 39619416, PMCID: PMC11605544, DOI: 10.1093/ve/veae091.Peer-Reviewed Original ResearchViral taxaRNA virusesAnalysis of metagenomic dataPlasmodium speciesSingle-celled eukaryotesHuman-infecting Plasmodium speciesPathogen life cycleGenome architectureGroup of virusesMetagenomic dataMetagenomic sequencingDisease-causingVirus discoveryTaxaViral diversityParasite PlasmodiumRNAInfecting protozoaPlasmodium knowlesiViromeHuman malariaParasite fitnessSpeciesApicomplexaInfect humansNo evidence that mutations in SARS-CoV-2 variants of concern derive from homologous fragments in gut microbiota
Parry R, Lytras S, Petrone M, Wille M, Crits-Christoph A, Gifford R, Saito A, Smura T, Peacock T. No evidence that mutations in SARS-CoV-2 variants of concern derive from homologous fragments in gut microbiota. Journal Of Virology 2024, 98: e01468-24. PMID: 39494907, PMCID: PMC11650967, DOI: 10.1128/jvi.01468-24.Peer-Reviewed Original ResearchBacterial sequencesViral RNA-dependent RNA polymeraseRNA-dependent RNA polymeraseSARS-CoV-2 variantsBacterial protein sequencesSARS-CoV-2 proteinsEvolution of mutationsRNA polymeraseIntrahost diversityProtein sequencesHomologous fragmentsNucleotide sequenceProtein databaseTemplate-switchingGut microbiotaSARS-CoV-2 VOCsViral genomeSARS-CoV-2Mutated fragmentsAmino acidsRdRpMutationsSequenceViral replicationProteinA ~40-kb flavi-like virus does not encode a known error-correcting mechanism
Petrone M, Grove J, Mélade J, Mifsud J, Parry R, Marzinelli E, Holmes E. A ~40-kb flavi-like virus does not encode a known error-correcting mechanism. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2403805121. PMID: 39018195, PMCID: PMC11287256, DOI: 10.1073/pnas.2403805121.Peer-Reviewed Original ResearchConceptsFlavi-like virusGenome sizeRNA virusesRNA virus genomesNucleic acid metabolismGenome lengthPhylogenetic inferenceDeleterious mutationsExonuclease domainGenomeVirus genomeProofreading mechanismPopulation extinctionMutation rateRNAAcid metabolismExonucleaseMutationsVirusMetatranscriptomicsStructural analysisLineagesProofreadingMechanismMetabolismDengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus
Vogels C, Hill V, Breban M, Chaguza C, Paul L, Sodeinde A, Taylor-Salmon E, Ott I, Petrone M, Dijk D, Jonges M, Welkers M, Locksmith T, Dong Y, Tarigopula N, Tekin O, Schmedes S, Bunch S, Cano N, Jaber R, Panzera C, Stryker I, Vergara J, Zimler R, Kopp E, Heberlein L, Herzog K, Fauver J, Morrison A, Michael S, Grubaugh N. DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus. BMC Genomics 2024, 25: 433. PMID: 38693476, PMCID: PMC11062901, DOI: 10.1186/s12864-024-10350-x.Peer-Reviewed Original ResearchConceptsAmplicon sequencing protocolsPrimer schemeSequencing protocolGenomic surveillanceDengue virus serotypesAmplicon sequencing workflowClinical specimensHigh genome coverageWhole-genome sequencingDengue virusVirus serotypesGenome coverageVirus stocksGenetic diversitySequencing instrumentsSequencing workflowGenotype VIDiverse serotypesSequence of samplesGenotype IVPrimersSurveillance of dengue virusSerotypesVirus copiesSerotype-specific
2023
Evidence for an ancient aquatic origin of the RNA viral order Articulavirales
Petrone M, Parry R, Mifsud J, Van Brussel K, Voorhees I, Richards Z, Holmes E. Evidence for an ancient aquatic origin of the RNA viral order Articulavirales. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2310529120. PMID: 37906647, PMCID: PMC10636315, DOI: 10.1073/pnas.2310529120.Peer-Reviewed Original ResearchConceptsEvolutionary historyAquatic-terrestrial transitionsDeep phylogenetic historiesVirus-host codivergenceMajor evolutionary transitionsLong-term evolutionary processesTotal RNA sequencingClose phylogenetic relationshipTranscriptome data miningPhylogenetic diversityEvolutionary transitionsPhylogenetic historyPhylogenetic relationshipsInfluenza virus lineagesPhylum CnidariaDivergent familiesPutative familiesRNA sequencingAquatic animalsEvolutionary processesNew hostAquatic originDisease-causing virusesEmergence of virusesVirus lineages
2022
Evaluation of saliva self-collection devices for SARS-CoV-2 diagnostics
Allicock OM, Petrone ME, Yolda-Carr D, Breban M, Walsh H, Watkins AE, Rothman JE, Farhadian SF, Grubaugh ND, Wyllie AL. Evaluation of saliva self-collection devices for SARS-CoV-2 diagnostics. BMC Infectious Diseases 2022, 22: 284. PMID: 35337266, PMCID: PMC8953967, DOI: 10.1186/s12879-022-07285-7.Peer-Reviewed Original ResearchComparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA
Earnest R, Uddin R, Matluk N, Renzette N, Turbett SE, Siddle KJ, Loreth C, Adams G, Tomkins-Tinch CH, Petrone ME, Rothman JE, Breban MI, Koch RT, Billig K, Fauver JR, Vogels CBF, Bilguvar K, De Kumar B, Landry ML, Peaper DR, Kelly K, Omerza G, Grieser H, Meak S, Martha J, Dewey HB, Kales S, Berenzy D, Carpenter-Azevedo K, King E, Huard RC, Novitsky V, Howison M, Darpolor J, Manne A, Kantor R, Smole SC, Brown CM, Fink T, Lang AS, Gallagher GR, Pitzer VE, Sabeti PC, Gabriel S, MacInnis BL, Team N, Altajar A, DeJesus A, Brito A, Watkins A, Muyombwe A, Blumenstiel B, Neal C, Kalinich C, Liu C, Loreth C, Castaldi C, Pearson C, Bernard C, Nolet C, Ferguson D, Buzby E, Laszlo E, Reagan F, Vicente G, Rooke H, Munger H, Johnson H, Tikhonova I, Ott I, Razeq J, Meldrim J, Brown J, Wang J, Vostok J, Beauchamp J, Grimsby J, Hall J, Messer K, Larkin K, Vernest K, Madoff L, Green L, Webber L, Gagne L, Ulcena M, Ray M, Fisher M, Barter M, Lee M, DeFelice M, Cipicchio M, Smith N, Lennon N, Fitzgerald N, Kerantzas N, Hui P, Harrington R, Downing R, Haye R, Lynch R, Anderson S, Hennigan S, English S, Cofsky S, Clancy S, Mane S, Ash S, Baez S, Fleming S, Murphy S, Chaluvadi S, Alpert T, Rivard T, Schulz W, Mandese Z, Tewhey R, Adams M, Park D, Lemieux J, Grubaugh N. Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA. Cell Reports Medicine 2022, 3: 100583. PMID: 35480627, PMCID: PMC8913280, DOI: 10.1016/j.xcrm.2022.100583.Peer-Reviewed Original ResearchConceptsEnhanced transmissibilitySARS-CoV-2 variant DeltaSARS-CoV-2 Delta variantViral RNA copiesPublic health programsAlpha infectionDelta infectionEffective reproductive numberDelta variantHealth programsVariant DeltaRNA copiesInfectionAlphaReproductive numberTransmissibilityEpidemiological dynamicsSequencing SARS-CoV-2 genomes from saliva
Alpert T, Vogels CBF, Breban MI, Petrone ME, Wyllie A, Grubaugh N, Fauver J. Sequencing SARS-CoV-2 genomes from saliva. Virus Evolution 2022, 8: veab098. PMID: 35542310, PMCID: PMC9074962, DOI: 10.1093/ve/veab098.Peer-Reviewed Original Research
2021
A stem-loop RNA RIG-I agonist protects against acute and chronic SARS-CoV-2 infection in mice
Mao T, Israelow B, Lucas C, Vogels CBF, Gomez-Calvo ML, Fedorova O, Breban MI, Menasche BL, Dong H, Linehan M, Alpert T, Anderson F, Earnest R, Fauver J, Kalinich C, Munyenyembe K, Ott I, Petrone M, Rothman J, Watkins A, Wilen C, Landry M, Grubaugh N, Pyle A, Iwasaki A. A stem-loop RNA RIG-I agonist protects against acute and chronic SARS-CoV-2 infection in mice. Journal Of Experimental Medicine 2021, 219: e20211818. PMID: 34757384, PMCID: PMC8590200, DOI: 10.1084/jem.20211818.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionChronic SARS-CoV-2 infectionVariants of concernLethal SARS-CoV-2 infectionPost-infection therapyLower respiratory tractPost-exposure treatmentType I interferonSARS-CoV-2Effective medical countermeasuresAdaptive immune systemBroad-spectrum antiviralsContext of infectionSingle doseRespiratory tractViral controlImmunodeficient miceSevere diseaseMouse modelI interferonViral infectionImmune systemInnate immunityDisease preventionConsiderable efficacy